This report provides some basic description of the peptide identificaiton from database search. Users can use this to quickly check the overal quality of the experiment Users can download the clean peptide quantification matrix for downstream analysis
Number of contaminant: 27
Number of reversed: 52
Number of qualified peptides: 16313
Number of quailfied peptide without intensity information(0 intensitiy): 695
Number of experiment: 24
All experiments: Xu_MLIspin_test_B6, Xu_MLIspin_test_B7, Xu_MLIspin_test_B8, Xu_MLIspin_test_B9, Xu_MLIspin_test_C6, Xu_MLIspin_test_C7, Xu_MLIspin_test_C8, Xu_MLIspin_test_C9, Xu_MLIspin_test_D6, Xu_MLIspin_test_D7, Xu_MLIspin_test_D8, Xu_MLIspin_test_D9, Xu_MLIspin_test_E6, Xu_MLIspin_test_E7, Xu_MLIspin_test_E8, Xu_MLIspin_test_E9, Xu_MLIspin_test_F6, Xu_MLIspin_test_F7, Xu_MLIspin_test_F8, Xu_MLIspin_test_F9, Xu_MLIspin_test_G6, Xu_MLIspin_test_G7, Xu_MLIspin_test_G8, Xu_MLIspin_test_G9
No meta information provided
Why charge state?
In a typical ESI analysis of trytic digest, most of the peptides should have 2 charges, less peptides have 3 charges, because tryptic peptides have a lysine/arginie at the C-terminal, along with N-terminal contributing another charge. A possible miscleavage will contribute the third charge.
It might indcate in-sufficient trypsin digesion, check the percentage of peptides with mis-cleavage site.
It migtht indcate the ESI is not sufficient/good enough.Check the distance between the ESI tip and MS oriface, if the ESI tip is dirty, if there is droplet occasionally.
Why peptide length do you expect?
Why peptide length do you expect?
In most cases, label-free quantification provides a decent way for metaproteomics profiling.
The more peptide of 100% presence the better
Figure shows how many peptides have more than N presence, which helps to set the presence cutoff
The table is clean peptides expression table, with reversed and contaminant removed. The values are the LFQ(with label free quantification turned on) or raw protein intensity from Maxquant output. You can download/export and start from this table for downstream analysis using the (i)Metalab faminly apps.
The talbe can be further visualized by our shiny apps shiny.imetalab.ca